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        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2016-04-29, 12:04 based on data in: /Users/philewels/Work/MultiQC_website/public_html/examples/wgs/data


        General Statistics

        Showing 6 rows.
        Sample NameChange rateTs/TvM VariantsAvg. GCInsert Size≥ 30XCoverageAlignedTotal Reads% Dups% Dups% GCLengthM Seqs
        P4107_1001
        764.0
        2.0
        4.1
        41%
        358
        74.7%
        36.0
        751.1
        772.1
        6.4%
        3.7%
        41%
        151
        383.6
        P4107_1002
        762.0
        2.0
        4.1
        41%
        367
        82.3%
        40.0
        847.1
        866.0
        9.9%
        2.2%
        41%
        151
        430.2
        P4107_1003
        761.0
        2.0
        4.1
        41%
        365
        82.4%
        40.0
        847.6
        868.2
        10.5%
        4.8%
        41%
        151
        431.4
        P4107_1004
        765.0
        2.0
        4.1
        41%
        363
        84.7%
        46.0
        985.1
        1002.8
        39.4%
        1.8%
        40%
        151
        498.2
        P4107_1005
        762.0
        2.0
        4.1
        41%
        368
        85.3%
        45.0
        955.9
        975.0
        24.5%
        6.6%
        41%
        151
        484.2
        P4107_1006
        761.0
        2.0
        4.1
        41%
        362
        84.1%
        43.0
        895.0
        912.4
        12.4%
        1.8%
        41%
        151
        453.2

        SnpEff

        SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

        Effects by Impact

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        Effects by Class

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        Counts by Effect

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        Counts by Genomic Region

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        Qualities

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        QualiMap

        QualiMap is a platform-independent application to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

        Coverage Histogram

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        Insert size Histogram

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        Genome Fraction Coverage

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        GC-content distribution

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        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Mark Duplicates

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        FastQ Screen

        FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Quality Histograms

        The mean quality value across each base position in the read. See the FastQC help.

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        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

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        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

        Click a heatmap row to see a line plot for that dataset.

        rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called. See the FastQC help.

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        Sequence Length Distribution

        All samples have sequences of exactly 151 bp in length.


        Sequence Duplication Levels

        The relative level of duplication found for every sequence. See the FastQC help.

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        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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